Name: rs58262369
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs58262369

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr14:64227194 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.033518 (8872/264690, TOPMED)
T=0.024310 (3410/140272, GnomAD)
T=0.06173 (4858/78692, PAGE_STUDY) (+ 15 more)
T=0.01100 (341/30986, ALFA)
T=0.06681 (1888/28258, 14KJPN)
T=0.06784 (1137/16760, 8.3KJPN)
T=0.0456 (292/6404, 1000G_30x)
T=0.0451 (226/5008, 1000G)
T=0.0011 (5/4480, Estonian)
T=0.0005 (2/3854, ALSPAC)
T=0.0000 (0/3708, TWINSUK)
T=0.0867 (254/2930, KOREAN)
T=0.0857 (157/1832, Korea1K)
T=0.014 (3/216, Qatari)
T=0.071 (15/212, Vietnamese)
C=0.47 (27/58, SGDP_PRJ)
C=0.5 (3/6, Siberian)
T=0.5 (3/6, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ESR2 : Non Coding Transcript Variant
LOC124903328 : 2KB Upstream Variant
Publications: 1 citation
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	30986	C=0.98900	T=0.01100
European	Sub	24820	C=0.99940	T=0.00060
African	Sub	3602	C=0.9484	T=0.0516
African Others	Sub	124	C=0.968	T=0.032
African American	Sub	3478	C=0.9477	T=0.0523
Asian	Sub	162	C=0.870	T=0.130
East Asian	Sub	134	C=0.888	T=0.112
Other Asian	Sub	28	C=0.79	T=0.21
Latin American 1	Sub	168	C=0.970	T=0.030
Latin American 2	Sub	700	C=0.897	T=0.103
South Asian	Sub	120	C=0.992	T=0.008
Other	Sub	1414	C=0.9710	T=0.0290

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.966482	T=0.033518
gnomAD - Genomes	Global	Study-wide	140272	C=0.975690	T=0.024310
gnomAD - Genomes	European	Sub	75964	C=0.99866	T=0.00134
gnomAD - Genomes	African	Sub	42048	C=0.95065	T=0.04935
gnomAD - Genomes	American	Sub	13658	C=0.93820	T=0.06180
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.9988	T=0.0012
gnomAD - Genomes	East Asian	Sub	3128	C=0.8971	T=0.1029
gnomAD - Genomes	Other	Sub	2154	C=0.9708	T=0.0292
The PAGE Study	Global	Study-wide	78692	C=0.93827	T=0.06173
The PAGE Study	AfricanAmerican	Sub	32512	C=0.95337	T=0.04663
The PAGE Study	Mexican	Sub	10810	C=0.87660	T=0.12340
The PAGE Study	Asian	Sub	8314	C=0.9180	T=0.0820
The PAGE Study	PuertoRican	Sub	7916	C=0.9396	T=0.0604
The PAGE Study	NativeHawaiian	Sub	4534	C=0.9493	T=0.0507
The PAGE Study	Cuban	Sub	4230	C=0.9820	T=0.0180
The PAGE Study	Dominican	Sub	3828	C=0.9705	T=0.0295
The PAGE Study	CentralAmerican	Sub	2450	C=0.9200	T=0.0800
The PAGE Study	SouthAmerican	Sub	1982	C=0.9102	T=0.0898
The PAGE Study	NativeAmerican	Sub	1260	C=0.9571	T=0.0429
The PAGE Study	SouthAsian	Sub	856	C=0.999	T=0.001
Allele Frequency Aggregator	Total	Global	30986	C=0.98900	T=0.01100
Allele Frequency Aggregator	European	Sub	24820	C=0.99940	T=0.00060
Allele Frequency Aggregator	African	Sub	3602	C=0.9484	T=0.0516
Allele Frequency Aggregator	Other	Sub	1414	C=0.9710	T=0.0290
Allele Frequency Aggregator	Latin American 2	Sub	700	C=0.897	T=0.103
Allele Frequency Aggregator	Latin American 1	Sub	168	C=0.970	T=0.030
Allele Frequency Aggregator	Asian	Sub	162	C=0.870	T=0.130
Allele Frequency Aggregator	South Asian	Sub	120	C=0.992	T=0.008
14KJPN	JAPANESE	Study-wide	28258	C=0.93319	T=0.06681
8.3KJPN	JAPANESE	Study-wide	16760	C=0.93216	T=0.06784
1000Genomes_30x	Global	Study-wide	6404	C=0.9544	T=0.0456
1000Genomes_30x	African	Sub	1786	C=0.9406	T=0.0594
1000Genomes_30x	Europe	Sub	1266	C=0.9992	T=0.0008
1000Genomes_30x	South Asian	Sub	1202	C=0.9967	T=0.0033
1000Genomes_30x	East Asian	Sub	1170	C=0.9128	T=0.0872
1000Genomes_30x	American	Sub	980	C=0.919	T=0.081
1000Genomes	Global	Study-wide	5008	C=0.9549	T=0.0451
1000Genomes	African	Sub	1322	C=0.9395	T=0.0605
1000Genomes	East Asian	Sub	1008	C=0.9157	T=0.0843
1000Genomes	Europe	Sub	1006	C=0.9990	T=0.0010
1000Genomes	South Asian	Sub	978	C=0.997	T=0.003
1000Genomes	American	Sub	694	C=0.918	T=0.082
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9989	T=0.0011
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9995	T=0.0005
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=1.0000	T=0.0000
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.9133	T=0.0867
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9143	T=0.0857
Qatari	Global	Study-wide	216	C=0.986	T=0.014
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.929	T=0.071
SGDP_PRJ	Global	Study-wide	58	C=0.47	T=0.53
Siberian	Global	Study-wide	6	C=0.5	T=0.5

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 14	NC_000014.9:g.64227194C>T
GRCh37.p13 chr 14	NC_000014.8:g.64693912C>T
SYNE2 RefSeqGene (LRG_872)	NG_011756.2:g.470296C>T
ESR2 RefSeqGene	NG_011535.1:g.116357G>A

Gene: ESR2, estrogen receptor 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ESR2 transcript variant b	NM_001040275.1:c.*339=	N/A	3 Prime UTR Variant
ESR2 transcript variant d	NM_001214902.1:c.*696=	N/A	3 Prime UTR Variant
ESR2 transcript variant l	NM_001291723.1:c.*339=	N/A	3 Prime UTR Variant
ESR2 transcript variant k	NM_001291712.2:c.*339=	N/A	3 Prime UTR Variant
ESR2 transcript variant f	NM_001271876.1:c.	N/A	Genic Downstream Transcript Variant
ESR2 transcript variant g	NM_001271877.1:c.	N/A	Genic Downstream Transcript Variant
ESR2 transcript variant a	NM_001437.3:c.	N/A	Genic Downstream Transcript Variant
ESR2 transcript variant h	NR_073496.2:n.2494G>A	N/A	Non Coding Transcript Variant
ESR2 transcript variant i	NR_073497.1:n.	N/A	Genic Downstream Transcript Variant
ESR2 transcript variant X1	XM_047431076.1:c.*696=	N/A	3 Prime UTR Variant
ESR2 transcript variant X2	XM_047431077.1:c.	N/A	Genic Downstream Transcript Variant
ESR2 transcript variant X3	XM_047431078.1:c.	N/A	Genic Downstream Transcript Variant

Gene: LOC124903328, uncharacterized LOC124903328 (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124903328 transcript	XR_007064205.1:n.	N/A	Upstream Transcript Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	C=	T
GRCh38.p14 chr 14	NC_000014.9:g.64227194=	NC_000014.9:g.64227194C>T
GRCh37.p13 chr 14	NC_000014.8:g.64693912=	NC_000014.8:g.64693912C>T
SYNE2 RefSeqGene (LRG_872)	NG_011756.2:g.470296=	NG_011756.2:g.470296C>T
ESR2 RefSeqGene	NG_011535.1:g.116357=	NG_011535.1:g.116357G>A
ESR2 transcript variant k	NM_001291712.2:c.*339=	NM_001291712.2:c.*339G>A
ESR2 transcript variant k	NM_001291712.1:c.*339=	NM_001291712.1:c.*339G>A
ESR2 transcript variant h	NR_073496.2:n.2494=	NR_073496.2:n.2494G>A
ESR2 transcript variant h	NR_073496.1:n.2431=	NR_073496.1:n.2431G>A
ESR2 transcript variant l	NM_001291723.1:c.*339=	NM_001291723.1:c.*339G>A
ESR2 transcript variant b	NM_001040275.1:c.*339=	NM_001040275.1:c.*339G>A
ESR2 transcript variant d	NM_001214902.1:c.*696=	NM_001214902.1:c.*696G>A
ESR2 transcript variant X1	XM_047431076.1:c.*696=	XM_047431076.1:c.*696G>A
ESR2 transcript variant j	NR_073505.1:n.2570=	NR_073505.1:n.2570G>A
ESR2 transcript variant c	NM_001040276.1:c.*339=	NM_001040276.1:c.*339G>A

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

55 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss83718109	Dec 15, 2007 (129)
2	BUSHMAN	ss200182160	Jul 04, 2010 (132)
3	1000GENOMES	ss226614956	Jul 14, 2010 (132)
4	1000GENOMES	ss243003293	Jul 15, 2010 (132)
5	ILLUMINA	ss481933518	May 04, 2012 (137)
6	ILLUMINA	ss483319391	May 04, 2012 (137)
7	ILLUMINA	ss534441847	Sep 08, 2015 (146)
8	TISHKOFF	ss564146252	Apr 25, 2013 (138)
9	SSMP	ss659830933	Apr 25, 2013 (138)
10	ILLUMINA	ss779319699	Sep 08, 2015 (146)
11	ILLUMINA	ss781605680	Sep 08, 2015 (146)
12	ILLUMINA	ss834787263	Sep 08, 2015 (146)
13	JMKIDD_LAB	ss1079725540	Aug 21, 2014 (142)
14	1000GENOMES	ss1351355213	Aug 21, 2014 (142)
15	EVA_UK10K_ALSPAC	ss1631922010	Apr 01, 2015 (144)
16	EVA_UK10K_TWINSUK	ss1674916043	Apr 01, 2015 (144)
17	EVA_DECODE	ss1695241376	Apr 01, 2015 (144)
18	HAMMER_LAB	ss1807961688	Sep 08, 2015 (146)
19	WEILL_CORNELL_DGM	ss1934612396	Feb 12, 2016 (147)
20	ILLUMINA	ss1959560976	Feb 12, 2016 (147)
21	GENOMED	ss1967982742	Jul 19, 2016 (147)
22	JJLAB	ss2028085266	Sep 14, 2016 (149)
23	USC_VALOUEV	ss2156461496	Dec 20, 2016 (150)
24	HUMAN_LONGEVITY	ss2202708265	Dec 20, 2016 (150)
25	SYSTEMSBIOZJU	ss2628533239	Nov 08, 2017 (151)
26	ILLUMINA	ss2633162464	Nov 08, 2017 (151)
27	GRF	ss2700889669	Nov 08, 2017 (151)
28	GNOMAD	ss2928695205	Nov 08, 2017 (151)
29	SWEGEN	ss3012342959	Nov 08, 2017 (151)
30	ILLUMINA	ss3021576974	Nov 08, 2017 (151)
31	ILLUMINA	ss3627239299	Oct 12, 2018 (152)
32	ILLUMINA	ss3631160034	Oct 12, 2018 (152)
33	ILLUMINA	ss3651970247	Oct 12, 2018 (152)
34	EGCUT_WGS	ss3679597152	Jul 13, 2019 (153)
35	EVA_DECODE	ss3696851813	Jul 13, 2019 (153)
36	ILLUMINA	ss3725455197	Jul 13, 2019 (153)
37	EVA	ss3752429061	Jul 13, 2019 (153)
38	PAGE_CC	ss3771794544	Jul 13, 2019 (153)
39	KHV_HUMAN_GENOMES	ss3817761862	Jul 13, 2019 (153)
40	SGDP_PRJ	ss3881691968	Apr 27, 2020 (154)
41	KRGDB	ss3930723984	Apr 27, 2020 (154)
42	KOGIC	ss3975099257	Apr 27, 2020 (154)
43	TOPMED	ss4973696883	Apr 27, 2021 (155)
44	TOMMO_GENOMICS	ss5213627598	Apr 27, 2021 (155)
45	1000G_HIGH_COVERAGE	ss5296530667	Oct 16, 2022 (156)
46	EVA	ss5315743792	Oct 16, 2022 (156)
47	EVA	ss5415825565	Oct 16, 2022 (156)
48	HUGCELL_USP	ss5490543045	Oct 16, 2022 (156)
49	EVA	ss5511273665	Oct 16, 2022 (156)
50	1000G_HIGH_COVERAGE	ss5596969033	Oct 16, 2022 (156)
51	SANFORD_IMAGENETICS	ss5656395643	Oct 16, 2022 (156)
52	TOMMO_GENOMICS	ss5766543844	Oct 16, 2022 (156)
53	YY_MCH	ss5814828664	Oct 16, 2022 (156)
54	EVA	ss5901693297	Oct 16, 2022 (156)
55	EVA	ss5947835071	Oct 16, 2022 (156)
56	1000Genomes	NC_000014.8 - 64693912	Oct 12, 2018 (152)
57	1000Genomes_30x	NC_000014.9 - 64227194	Oct 16, 2022 (156)
58	The Avon Longitudinal Study of Parents and Children	NC_000014.8 - 64693912	Oct 12, 2018 (152)
59	Genetic variation in the Estonian population	NC_000014.8 - 64693912	Oct 12, 2018 (152)
60	gnomAD - Genomes	NC_000014.9 - 64227194	Apr 27, 2021 (155)
61	KOREAN population from KRGDB	NC_000014.8 - 64693912	Apr 27, 2020 (154)
62	Korean Genome Project	NC_000014.9 - 64227194	Apr 27, 2020 (154)
63	The PAGE Study	NC_000014.9 - 64227194	Jul 13, 2019 (153)
64	Qatari	NC_000014.8 - 64693912	Apr 27, 2020 (154)
65	SGDP_PRJ	NC_000014.8 - 64693912	Apr 27, 2020 (154)
66	Siberian	NC_000014.8 - 64693912	Apr 27, 2020 (154)
67	8.3KJPN	NC_000014.8 - 64693912	Apr 27, 2021 (155)
68	14KJPN	NC_000014.9 - 64227194	Oct 16, 2022 (156)
69	TopMed	NC_000014.9 - 64227194	Apr 27, 2021 (155)
70	UK 10K study - Twins	NC_000014.8 - 64693912	Oct 12, 2018 (152)
71	A Vietnamese Genetic Variation Database	NC_000014.8 - 64693912	Jul 13, 2019 (153)
72	ALFA	NC_000014.9 - 64227194	Apr 27, 2021 (155)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss83718109, ss200182160, ss483319391, ss1695241376	NC_000014.7:63763664:C:T	NC_000014.9:64227193:C:T	(self)
64349211, 35749403, 25335400, 37901378, 16654326, 33708948, 8977850, 71596905, 35749403, 7953925, ss226614956, ss243003293, ss481933518, ss534441847, ss564146252, ss659830933, ss779319699, ss781605680, ss834787263, ss1079725540, ss1351355213, ss1631922010, ss1674916043, ss1807961688, ss1934612396, ss1959560976, ss1967982742, ss2028085266, ss2156461496, ss2628533239, ss2633162464, ss2700889669, ss2928695205, ss3012342959, ss3021576974, ss3627239299, ss3631160034, ss3651970247, ss3679597152, ss3752429061, ss3881691968, ss3930723984, ss5213627598, ss5315743792, ss5415825565, ss5511273665, ss5656395643, ss5947835071	NC_000014.8:64693911:C:T	NC_000014.9:64227193:C:T	(self)
84494968, 453722643, 31477258, 1016013, 100380948, 189242542, 4027064862, ss2202708265, ss3696851813, ss3725455197, ss3771794544, ss3817761862, ss3975099257, ss4973696883, ss5296530667, ss5490543045, ss5596969033, ss5766543844, ss5814828664, ss5901693297	NC_000014.9:64227193:C:T	NC_000014.9:64227193:C:T	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs58262369

PMID	Title	Author	Year	Journal
26443449	Large-scale association analysis in Asians identifies new susceptibility loci for prostate cancer.	Wang M et al.	2015	Nature communications

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
Top▲ Help
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs58262369